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comparison kronik.xml @ 6:73fc27617b2e draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
author galaxyp
date Tue, 07 Apr 2020 03:27:32 -0400
parents 539f157784e7
children
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5:c5b3b7eafd46 6:73fc27617b2e
1 <tool id="kronik" name="Kronik" version="2.20"> 1 <tool id="kronik" name="Kronik" version="2.20+galaxy1">
2 <description>processes Hardklor features to find peptides by chromatographic profiling</description> 2 <description>processes Hardklor features to find peptides by chromatographic profiling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.20">kronik</requirement> 4 <requirement type="package" version="2.20">kronik</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/> 7 <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/>
8 </stdio> 8 </stdio>
9 <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command> 9 <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p '$inputfile' '$output'</command>
10 <inputs> 10 <inputs>
11 <param name="inputfile" type="data" format="hardklor" label="Hardklör isotope distributions" /> 11 <param name="inputfile" type="data" format="hardklor" label="Hardklör isotope distributions" />
12 <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" /> 12 <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" />
13 <param name="d" type="integer" value="3" label="Match tolerance" help="Minimum consecutive scans peptide must be found in" /> 13 <param name="d" type="integer" value="3" label="Match tolerance" help="Minimum consecutive scans peptide must be found in" />
14 <param name="g" type="integer" value="1" label="Gap tolerance" help="Maximum amount of scans a peptide can skip to be considered in results" /> 14 <param name="g" type="integer" value="1" label="Gap tolerance" help="Maximum amount of scans a peptide can skip to be considered in results" />