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comparison pepquery2_index.xml @ 0:24681d6372f3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author galaxyp
date Sun, 06 Nov 2022 16:26:04 +0000
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1 <tool id="pepquery2_index" name="PepQuery2 index" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>MS/MS data for faster search</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 @CMD_IMPORTS@
11 @INDEX_SPECTRUM_FILES@
12 $index_spectrum_files($output.files_path, $inputs)
13 ]]></command>
14 <inputs>
15 <param name="inputs" argument="-i" type="data" format="mfg,mzml,mzxml" multiple="true" label="MS Spectrum files">
16 </param>
17 </inputs>
18 <outputs>
19 <data name="output" format="txt" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="index_dir/summary.txt"/>
20 </outputs>
21 <tests>
22 <test>
23 <param name="inputs" ftype="mzml" value="small-index-filter.mzML"/>
24 <output name="output">
25 <assert_contents>
26 <has_text text="small-index-filter.mzML"/>
27 </assert_contents>
28 </output>
29 </test>
30 <test>
31 <param name="inputs" value="small-index-filter.mzML,AgilentMassHunterTest.mzXML,immunopeptidomics.mgf"/>
32 <output name="output">
33 <assert_contents>
34 <has_text text="small-index-filter.mzML"/>
35 <has_text text="AgilentMassHunterTest.mzXML"/>
36 <has_text text="immunopeptidomics.mgf"/>
37 </assert_contents>
38 </output>
39 </test>
40 </tests>
41 <help><![CDATA[
42 **PepQuery Index**
43
44 Indexes MS/MS data for fast searching.
45 This can significant speed up the search especially when the size of MS/MS data is very large.
46
47 The output can be used as input to **PepQuery2** Galaxy tool in the **MS/MS dataset to search** *Indexed MS/MS spectrums*.
48 ]]></help>
49 <expand macro="citations" />
50 </tool>