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comparison fasta_cli.xml @ 55:bb0130ff73ce draft

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"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
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children da885ca16cb2
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54:7fdd9119cc4f 55:bb0130ff73ce
1 <tool id="fasta_cli" name="FastaCLI" version="1.0.1">
2 <description>
3 Appends decoy sequences to FASTA files
4 </description>
5 <macros>
6 <import>macros_basic.xml</import>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
10 </requirements>
11 <expand macro="stdio" />
12 <command>
13 <![CDATA[
14 #set $temp_stderr = "fasta_cli_stderr"
15 #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
16
17 mkdir output &&
18 cwd=`pwd` &&
19
20 echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}' &&
21 cp '${input_database}' '${input_database.display_name}' &&
22
23 ###########################################
24 #### Creating decoy database ####
25 ###########################################
26
27 echo 'Creating decoy database.' &&
28 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${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>> $temp_stderr &&
29 mv '${output_db_name}' output &&
30 cat $temp_stderr 2>&1;
31 ]]>
32 </command>
33 <inputs>
34 <param format="fasta" name="input_database" type="data" label="Protein Database"
35 help="Select FASTA database from history"/>
36
37 <section name="database_processing_options" expanded="true" title="Database Processing Options">
38
39 <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
40 </param>
41 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
42 <option value="1">Prefix</option>
43 <option value="2" selected="True">Suffix</option>
44 </param>
45
46 <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix">
47 </param>
48
49 </section>
50 </inputs>
51 <outputs>
52 <data name="input_database_concatenated_target_decoy" format="fasta" label="${tool.name}: ${input_database.display_name} with decoys on ${on_string}">
53 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" directory="output" visible="true" format="fasta" assign_primary_output="true" />
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
59 <output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
60 </test>
61 </tests>
62 <help>
63 **What it does**
64
65 Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie:
66
67 * Decoy flag: -REVERSED
68
69 * Location: suffix
70
71 * Target decoy suffix: _concatenated_target_decoy
72
73 </help>
74 <expand macro="citations" />
75 </tool>