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comparison macros.xml @ 2:ef46866326ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit e75f095a55caa325cd97127114c9703e4557ad50
author galaxyp
date Tue, 16 Jul 2024 06:55:53 +0000
parents dc5de2ea607e
children da9ebef968bd
comparison
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1:dc5de2ea607e 2:ef46866326ef
1 <macros> 1 <macros>
2 <import>msfragger_macros.xml</import> 2 <import>msfragger_macros.xml</import>
3 <token name="@TOOL_VERSION@">20.0</token> 3 <token name="@TOOL_VERSION@">20.0</token>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">2</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
18 18
19 User must also supply their own manifest file, a TSV file of the format: 19 User must also supply their own manifest file, a TSV file of the format:
20 name, experiment, bioreplicate, data type 20 name, experiment, bioreplicate, data type
21 --> 21 -->
22 <xml name="samples"> 22 <xml name="samples">
23 <param name="inputs" type="data" format="mzml,mzxml" multiple="true" label="Proteomics Spectrum files" help="All input scan files must of a matching format: mzML, mzXML"/> 23 <param name="inputs" type="data" format="mzml,mzxml,thermo.raw" multiple="true" label="Proteomics Spectrum files" help="All input scan files must be named with one of the following extensions: .mzML, .mzXML, or .raw"/>
24 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs"> 24 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
25 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator> 25 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
26 </param> 26 </param>
27 <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be mzML or mzXML.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/> 27 <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be .mzML, .mzXML, or .raw.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
28 </xml> 28 </xml>
29 29
30 <!-- 30 <!--
31 Prepares enviroment variables for FragPipe. 31 Prepares enviroment variables for FragPipe.
32 --> 32 -->