Mercurial > repos > jjohnson > encyclopedia_library_to_blib
comparison encyclopedia_library_to_blib.xml @ 0:058db6d8a1b3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author | jjohnson |
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date | Fri, 19 Jun 2020 10:13:33 -0400 |
parents | |
children | 4850741d1dff |
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-1:000000000000 | 0:058db6d8a1b3 |
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1 <tool id="encyclopedia_library_to_blib" name="ConvertLibraryToBlib" version="@VERSION@.0" python_template_version="3.5"> | |
2 <description>Convert EncyclopeDIA Library to BLIB for Skyline</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 EncyclopeDIA -convert -libtoblib | |
9 -i '$i' | |
10 -o '$output' | |
11 #if $istest == 'yes' | |
12 && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output' | |
13 #end if | |
14 ]]></command> | |
15 <inputs> | |
16 <param argument="-i" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/> | |
17 <param name="istest" type="hidden" value="no"/> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="output" format="blib" label="${i.name} blib"/> | |
21 <data name="test_output" format="txt" > | |
22 <filter>istest == 'yes'</filter> | |
23 </data> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="i" ftype="dlib" value="PrositLib.dlib"/> | |
28 <param name="istest" value="yes"/> | |
29 <output name="test_output" ftype="txt"> | |
30 <assert_contents> | |
31 <has_text text="AGGVLHDDENLWSFGK"/> | |
32 </assert_contents> | |
33 </output> | |
34 </test> | |
35 </tests> | |
36 <help><![CDATA[ | |
37 Convert EncyclopeDIA Library to BLIB for Skyline. | |
38 ]]></help> | |
39 <expand macro="citations" /> | |
40 </tool> |