Mercurial > repos > galaxyp > fastg2protlib

comparison fastg2protlib-validate.xml @ 0:25dd9931d6b1 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
author galaxyp
date Fri, 07 Aug 2020 10:16:55 +0000
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1 <tool id="fastg2protlib-validate" name="FASTG2Protlib-Validate" version="@VERSION@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="pkg_requirement" />
6 <description>Validate a candidate protein library</description>
7
8 <command detect_errors="exit_code">
9 <![CDATA[
10 python '$__tool_directory__/app_validate.py'
11 -d '$database_file'
12 -f $fdr_level
13 -x '$decoy_header'
14 '$tabular_file'
15 ]]>
16 </command>
17 <inputs>
18 <param name="tabular_file" type="data" format="txt" label="MSGF+ tabular file" />
19 <param name="database_file" type="data" format="sqlite" label="Database Name"/>
20 <param name="fdr_level" type="float" value="0.10" label="FDR value for validation."/>
21 <param name="decoy_header" type="text" value="XXX_" label="Decoy protein header"/>
22 </inputs>
23 <outputs>
24 <data name="protein_fasta" format="fasta" from_work_dir="protein.fasta" label="Validated protein library"/>
25 <data name="protein_score" format="csv" from_work_dir="protein_scores.csv" label="Protein scores"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="tabular_file" value="mgf_tst.tab" />
30 <param name="database_file" value="tst_valid.db" />
31 <param name="fdr_level" value="0.10" />
32 <param name="decoy_header" value="XXX_" />
33 <output name="protein_fasta">
34 <assert_contents>
35 <has_text text="RYSRPLSHL" />
36 </assert_contents>
37 </output>
38 </test>
39 </tests>
40 <expand macro="help-text" />
41 </tool>