Mercurial > repos > tomnl > mspurity_frag4feature

comparison frag4feature.xml @ 15:a2ba12977060 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 12:35:23 +0000
parents 274dc7b40bc2
children
comparison
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14:64431b9affe2 15:a2ba12977060
1 <tool id="mspurity_frag4feature" name="msPurity.frag4feature" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> 1 <tool id="mspurity_frag4feature" name="msPurity.frag4feature" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> 2 <description>
3 Assign fragmentation spectra to XCMS features using msPurity 3 Assign fragmentation spectra to XCMS features using msPurity
4 </description> 4 </description>
5
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9 8 <expand macro="requirements"/>
10 <expand macro="requirements"> 9 <command detect_errors="exit_code"><![CDATA[
11 </expand> 10 Rscript '$__tool_directory__/frag4feature.R'
12 <stdio>
13 <exit_code range="1:" />
14 </stdio>
15 <command interpreter="Rscript"><![CDATA[
16 frag4feature.R
17 --out_dir=. 11 --out_dir=.
18 --xset=$xset 12 --xset='$xset'
19 --pa=$pa 13 --pa='$pa'
20 --cores=\${GALAXY_SLOTS:-4} 14 --cores=\${GALAXY_SLOTS:-4}
21 #if $file_load_conditional.file_load_select=="yes" 15 #if $file_load_conditional.file_load_select=="yes"
22 --mzML_files=' 16 --mzML_files='
23 #for $i in $file_load_conditional.input 17 #for $i in $file_load_conditional.input
24 $i, 18 $i,
45 39
46 40
47 ]]></command> 41 ]]></command>
48 <inputs> 42 <inputs>
49 43
50 <param type="data" name="xset" label="xcmsSet object" argument="--xset" 44 <param argument="--xset" type="data" label="xcmsSet object"
51 help="grouped xcmsSet object saved as 'xset' in an RData file" 45 help="grouped xcmsSet object saved as 'xset' in an RData file"
52 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> 46 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
53 <param type="data" name="pa" label="purityA object" format="rdata" argument="--pa" 47 <param argument="--pa" type="data" label="purityA object" format="rdata"
54 help="purityA object generated from msPurity_purityA. 48 help="purityA object generated from msPurity_purityA.
55 Contains details of fragmentation spectra and precursor ion purity results 49 Contains details of fragmentation spectra and precursor ion purity results
56 (output from purityA tool)"/> 50 (output from purityA tool)"/>
57 <param name="ppm" type="float" argument="--ppm" value="10" 51 <param argument="--ppm" type="float" value="10"
58 label="ppm error tolerance between precursor mz and XCMS feature mz" 52 label="ppm error tolerance between precursor mz and XCMS feature mz"
59 help="Fragmentation will be ignored if the precursor mz value is not within 53 help="Fragmentation will be ignored if the precursor mz value is not within
60 the ppm error tolerance to the XCMS feature mz"/> 54 the ppm error tolerance to the XCMS feature mz"/>
61 <param name="plim" type="float" label="Precursor ion purity threshold" 55 <param argument="--plim" type="float" label="Precursor ion purity threshold"
62 value="0" max="1" min="0" argument="--plim" 56 value="0" max="1" min="0"
63 help="Fragmentation will be ignore if the precursor ion purity is less than the 57 help="Fragmentation will be ignore if the precursor ion purity is less than the
64 threshold (further filtering on the precursor ion purity can be done at the averaging 58 threshold (further filtering on the precursor ion purity can be done at the averaging
65 stage if required)."/> 59 stage if required)."/>
66 <param name="intense" type="boolean" checked="true" argument="--intense" 60 <param argument="--intense" type="boolean" checked="true"
67 label="Should the most intense precursor be used within the isolation window?" 61 label="Should the most intense precursor be used within the isolation window?"
68 help="If TRUE the most intense precursor will be used. If FALSE the precursor 62 help="If TRUE the most intense precursor will be used. If FALSE the precursor
69 closest to the center of the isolation window will be used"/> 63 closest to the center of the isolation window will be used"/>
70 <param name="convert2RawRT" type="boolean" checked="false" argument="--convert2RawRT" 64 <param argument="--convert2RawRT" type="boolean" checked="false"
71 label="Was retention time correction used?" 65 label="Was retention time correction used?"
72 help="If retention time correction has been used in XCMS set this to yes"/> 66 help="If retention time correction has been used in XCMS set this to yes"/>
73 <param name="useGroup" type="boolean" checked="false" argument="--useGroup" 67 <param argument="--useGroup" type="boolean" checked="false"
74 label="For matching fragmentation to a feature, use the grouped feature range" 68 label="For matching fragmentation to a feature, use the grouped feature range"
75 help="For special cases where the MS2 files have no MS1 data or if the MS1 data in the MS2 file is unreliable" /> 69 help="For special cases where the MS2 files have no MS1 data or if the MS1 data in the MS2 file is unreliable" />
76 70
77 <expand macro="fileload" /> 71 <expand macro="fileload" />
78 72