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comparison kronik.xml @ 4:539f157784e7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 975141c5e10d414c44d5e4172d9cbd5e3e6a1abe
author galaxyp
date Sat, 08 Apr 2017 08:17:22 -0400
parents a979b9ff3272
children 73fc27617b2e
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3:a979b9ff3272 4:539f157784e7
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="hk" 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" />
15 <param name="m" type="integer" value="8000" label="Max mass (Da)" help="Maximum mass of peptide isotope distribution" /> 15 <param name="m" type="integer" value="8000" label="Max mass (Da)" help="Maximum mass of peptide isotope distribution" />
16 <param name="n" type="integer" value="600" label="Min mass (Da)" help="Minimum mass of peptide isotope distribution" /> 16 <param name="n" type="integer" value="600" label="Min mass (Da)" help="Minimum mass of peptide isotope distribution" />
17 <param name="p" type="integer" value="10" label="Mass accuracy (ppm)" help="Peptides in adjacent scans must differ by less than this value to be called the same." /> 17 <param name="p" type="integer" value="10" label="Mass accuracy (ppm)" help="Peptides in adjacent scans must differ by less than this value to be called the same." />
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data format="kr" name="output" /> 20 <data format="kronik" name="output" />
21 </outputs> 21 </outputs>
22 <tests> 22 <tests>
23 <test> 23 <test>
24 <param name="inputfile" value="hardklor_result.hk"/> 24 <param name="inputfile" value="hardklor_result.hk"/>
25 <output name="output" file="kronik_result.kr" /> 25 <output name="output" file="kronik_result.kr" />