Mercurial > repos > galaxyp > psm_validation
comparison psm_validation.xml @ 0:ddcab0f11473 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
author | galaxyp |
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date | Thu, 15 Oct 2020 07:45:17 +0000 |
parents | |
children | b71c651e7950 |
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-1:000000000000 | 0:ddcab0f11473 |
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1 <tool id="psmvalidator" name="PSM-Fragment Validator" version="@VERSION@"> | |
2 <macros> | |
3 <import>macros.xml</import> | |
4 </macros> | |
5 <description>Validate PSMs against Ion Fragmentation</description> | |
6 <expand macro="pkg_requirement" /> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/application.py' | |
10 -d '$mz_db_name' | |
11 -p '$peptide_sequences' | |
12 #if $neutral_loss_ions: | |
13 -n | |
14 #end if | |
15 #if $internal_ions: | |
16 -i | |
17 #end if | |
18 -b $b_ion_run | |
19 -y $y_ion_run | |
20 -e $epsilon | |
21 #if $b_ion_run < 0: | |
22 --test | |
23 #end if | |
24 ]]> | |
25 </command> | |
26 <inputs> | |
27 <param name="mz_db_name" type="data" format="mz.sqlite" label="MZSQLite DB" /> | |
28 <param name="peptide_sequences" type="data" format="tabular" label="Peptide Sequence List" /> | |
29 <param name="b_ion_run" type="integer" value="2" label="Consecutive B-Ions" /> | |
30 <param name="y_ion_run" type="integer" value="2" label="Consecutive Y-Ions" /> | |
31 <param name="neutral_loss_ions" type="boolean" checked="True" label="Use Neutral Loss" /> | |
32 <param name="internal_ions" type="boolean" checked="True" label="Use Internals" /> | |
33 <param name="epsilon" type="float" value="0.5" label="Epsilon" /> | |
34 </inputs> | |
35 <outputs> | |
36 <data name="html_output" format="html" from_work_dir="index.html" label="PSM Ion Fragementation Report" /> | |
37 <data name="text_output" format="tabular" from_work_dir="results.tab" label="Tabular Results" /> | |
38 </outputs> | |
39 <tests> | |
40 <test> | |
41 <param name="mz_db_name" value="test.db" /> | |
42 <param name="peptide_sequences" value="test-peptides.txt" /> | |
43 <param name="b_ion_run" value="-99" /> | |
44 <param name="y_ion_run" value="-99" /> | |
45 <param name="neutral_loss_ions" value="True" /> | |
46 <param name="internal_ions" value="True" /> | |
47 <param name="epsilon" value="0.5" /> | |
48 <output name="html_output"> | |
49 <assert_contents> | |
50 <has_text text="success" /> | |
51 </assert_contents> | |
52 </output> | |
53 </test> | |
54 </tests> | |
55 <expand macro="help-text" /> | |
56 </tool> |