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annotate 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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24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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1 <tool id="pepquery2_index" name="PepQuery2 index" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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2 <description>MS/MS data for faster search</description>
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3 <macros>
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4 <import>macros.xml</import>
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CMD_IMPORTS@
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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11 @INDEX_SPECTRUM_FILES@
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12 $index_spectrum_files($output.files_path, $inputs)
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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13 ]]></command>
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14 <inputs>
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15 <param name="inputs" argument="-i" type="data" format="mfg,mzml,mzxml" multiple="true" label="MS Spectrum files">
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="txt" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="index_dir/summary.txt"/>
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="inputs" ftype="mzml" value="small-index-filter.mzML"/>
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24 <output name="output">
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25 <assert_contents>
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26 <has_text text="small-index-filter.mzML"/>
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27 </assert_contents>
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28 </output>
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29 </test>
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30 <test>
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31 <param name="inputs" value="small-index-filter.mzML,AgilentMassHunterTest.mzXML,immunopeptidomics.mgf"/>
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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32 <output name="output">
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33 <assert_contents>
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34 <has_text text="small-index-filter.mzML"/>
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35 <has_text text="AgilentMassHunterTest.mzXML"/>
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36 <has_text text="immunopeptidomics.mgf"/>
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37 </assert_contents>
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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38 </output>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **PepQuery Index**
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43
24681d6372f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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44 Indexes MS/MS data for fast searching.
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45 This can significant speed up the search especially when the size of MS/MS data is very large.
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46
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47 The output can be used as input to **PepQuery2** Galaxy tool in the **MS/MS dataset to search** *Indexed MS/MS spectrums*.
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>