Mercurial > repos > tomnl > mspurity_filterfragspectra

comparison filterFragSpectra.xml @ 14:a9928d2ecde6 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:39:38 +0000
parents eeae5175cfed
children
comparison
equal deleted inserted replaced
13:bf057be0a1de 14:a9928d2ecde6
3 Filter fragmentations spectra associated with an XCMS feature 3 Filter fragmentations spectra associated with an XCMS feature
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements" />
9 </expand> 9 <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[
10 <stdio>
11 <exit_code range="1:" />
12 </stdio>
13 <command interpreter="Rscript"><![CDATA[
14 filterFragSpectra.R 10 filterFragSpectra.R
15 --out_rdata=$filterFragSpectra_output_rdata 11 --out_rdata='$filterFragSpectra_output_rdata'
16 --out_peaklist_prec=$filterFragSpectra_output_prec_tsv 12 --out_peaklist_prec='$filterFragSpectra_output_prec_tsv'
17 --out_peaklist_frag=$filterFragSpectra_output_frag_tsv 13 --out_peaklist_frag='$filterFragSpectra_output_frag_tsv'
18 --pa="$pa" 14 --pa='$pa'
19 --ilim=$ilim 15 --ilim=$ilim
20 --plim=$plim 16 --plim=$plim
21 --ra=$ra 17 --ra=$ra
22 --snr=$snr 18 --snr=$snr
23 --snmeth=$snmeth 19 --snmeth=$snmeth
24 $rmp 20 $rmp
25 ]]></command> 21 ]]></command>
26 <inputs> 22 <inputs>
27 <param name="pa" type="data" 23 <param argument="--pa" type="data"
28 label="purityA object with fragmentation linked to XCMS features" format="rdata" 24 label="purityA object with fragmentation linked to XCMS features" format="rdata"
29 help="purityA object saved as 'pa' in a RData file where fragmentation has 25 help="purityA object saved as 'pa' in a RData file where fragmentation has
30 been linked to XCMS features(output from frag4feature tool)"/> 26 been linked to XCMS features(output from frag4feature tool)"/>
31 <param name="plim" type="float" value="0.5" help="" 27 <param argument="--plim" type="float" value="0.5" help=""
32 label="Miniumum precursor ion purity of the associated precursor for 28 label="Miniumum precursor ion purity of the associated precursor for
33 fragmentation spectra scan" /> 29 fragmentation spectra scan" />
34 <param name="ilim" type="float" value="0.0" label="Peak instensity threshold" help="" /> 30 <param argument="--ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
35 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" 31 <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0"
36 label="Relative abundance threshold" help="" /> 32 label="Relative abundance threshold" help="" />
37 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" /> 33 <param argument="--snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
38 <param name="snmeth" type="select" label="Function to calculate noise." help="" > 34 <param argument="--snmeth" type="select" label="Function to calculate noise." help="" >
39 <option value="median" selected="true">median</option> 35 <option value="median" selected="true">median</option>
40 <option value="mean">mean</option> 36 <option value="mean">mean</option>
41 <!-- <option value="mad">mad</option> --> 37 <!-- <option value="mad">mad</option> -->
42 </param> 38 </param>
43 <param name="rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue="" 39 <param argument="--rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
44 label="Remove peaks that do not meet the filtering criteria. 40 label="Remove peaks that do not meet the filtering criteria.
45 Otherwise peaks will be flagged instead." 41 Otherwise peaks will be flagged instead."
46 help="" /> 42 help="" />
47 </inputs> 43 </inputs>
48 <outputs> 44 <outputs>
49 <data name="filterFragSpectra_output_rdata" format="rdata" 45 <data name="filterFragSpectra_output_rdata" format="rdata"
50 label="${tool.name} on ${on_string}: RData" /> 46 label="${tool.name} on ${on_string}: RData" />
51 <data name="filterFragSpectra_output_prec_tsv" format="tsv" 47 <data name="filterFragSpectra_output_prec_tsv" format="tsv"
52 label="${tool.name} on ${on_string}: peaklist (precursors)" /> 48 label="${tool.name} on ${on_string}: peaklist (precursors)" />
53 <data name="filterFragSpectra_output_frag_tsv" format="tsv" 49 <data name="filterFragSpectra_output_frag_tsv" format="tsv"
54 label="${tool.name} on ${on_string}: peaklist (fragments)" /> 50 label="${tool.name} on ${on_string}: peaklist (fragments)" />
55 </outputs> 51 </outputs>
56 <tests> 52 <tests>
57 <test> 53 <test>
58 <param name="pa" value="frag4feature_output.RData" /> 54 <param name="pa" value="frag4feature_output.RData" />
59 <output name="filterFragSpectra_output_rdata" 55 <output name="filterFragSpectra_output_rdata"
60 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" /> 56 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
61 <output name="filterFragSpectra_output_prec_tsv" 57 <output name="filterFragSpectra_output_prec_tsv"
62 file="filterFragSpectra_output_prec.tsv" ftype="tsv" /> 58 file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
63 <output name="filterFragSpectra_output_frag_tsv" 59 <output name="filterFragSpectra_output_frag_tsv"
64 file="filterFragSpectra_output_frag.tsv" ftype="tsv" /> 60 file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
65 </test> 61 </test>
66 </tests> 62 </tests>
67 63
68 <help><![CDATA[ 64 <help><![CDATA[