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comparison purityX.xml @ 15:8f4685455caf 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 12:32:11 +0000
parents 3ca9866b1d85
children
comparison
equal deleted inserted replaced
14:f078bb1b7da6 15:8f4685455caf
2 <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. 2 <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset.
3 </description> 3 </description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7
8 <expand macro="requirements" /> 7 <expand macro="requirements" />
9 8 <command detect_errors="exit_code"><![CDATA[
10 <stdio> 9 Rscript '$__tool_directory__/purityX.R'
11 <exit_code range="1:" /> 10 --xset_path='$xset'
12 </stdio> 11 --out_dir='.'
13 <command interpreter="Rscript"><![CDATA[
14 purityX.R
15 --xset_path=$xset
16 --out_dir=.
17 --minOffset=$minoffset 12 --minOffset=$minoffset
18 --maxOffset=$maxoffset 13 --maxOffset=$maxoffset
19 --singleFile=$singleFile 14 --singleFile=$singleFile
20 --purityType=$purityType 15 --purityType=$purityType
21 --cores=\${GALAXY_SLOTS:-4} 16 --cores=\${GALAXY_SLOTS:-4}
22 #if $xgroups.xgroups == "choose" 17 #if $xgroups.xgroups == "choose"
23 --xgroups=$xgroups.xgroups_value 18 --xgroups='$xgroups.xgroups_value'
24 #end if 19 #end if
25 --camera_xcms=$camera_xcms 20 --camera_xcms=$camera_xcms
26 #if $camera_xcms == "camera" 21 #if $camera_xcms == "camera"
27 --rdata_name=xa 22 --rdata_name=xa
28 #else 23 #else
32 --ilim=$ilim 27 --ilim=$ilim
33 #if $isotopes.isotopes == "exclude_default" 28 #if $isotopes.isotopes == "exclude_default"
34 --exclude_isotopes 29 --exclude_isotopes
35 #elif $isotopes.isotopes == "user" 30 #elif $isotopes.isotopes == "user"
36 --exclude_isotopes 31 --exclude_isotopes
37 --isotope_matrix=$isotopes.im 32 --isotope_matrix='$isotopes.im'
38 #end if 33 #end if
39 #if $file_load_conditional.file_load_select == 'yes' 34 #if $file_load_conditional.file_load_select == 'yes'
40 --galaxy_files=' 35 --galaxy_files='
41 #for $i in $file_load_conditional.input 36 #for $i in $file_load_conditional.input
42 $i, 37 $i,
64 59
65 60
66 ]]></command> 61 ]]></command>
67 <inputs> 62 <inputs>
68 63
69 <param type="data" name="xset" format="rdata" 64 <param argument="--xset" type="data" format="rdata"
70 help="xcmsSet object saved as an RData file"/> 65 help="xcmsSet object saved as an RData file"/>
71 <expand macro="offsets" /> 66 <expand macro="offsets" />
72 <expand macro="general_params" /> 67 <expand macro="general_params" />
73 <param name="singleFile" type="integer" label="singleFile" value="0" 68 <param argument="--singleFile" type="integer" label="singleFile" value="0"
74 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks). 69 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
75 Uses the index of the files in xcmsSet object. If zero this is ignored"/> 70 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
76 71
77 <conditional name="choose_class_cond"> 72 <conditional name="choose_class_cond">
78 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" > 73 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
80 <option value="all" selected="true">calculate average across all classes</option> 75 <option value="all" selected="true">calculate average across all classes</option>
81 </param> 76 </param>
82 <when value="all"> 77 <when value="all">
83 </when> 78 </when>
84 <when value="choose"> 79 <when value="choose">
85 <param name="class" type="text" label="Choose class" 80 <param argument="--class" type="text" label="Choose class"
86 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object 81 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
87 i.e. xset@phenoData). An average will across all the choosen classes." /> 82 i.e. xset@phenoData). An average will across all the choosen classes." />
88 </when> 83 </when>
89 </conditional> 84 </conditional>
90 85
91 <conditional name="ignore_files_cond"> 86 <conditional name="ignore_files_cond">
92 <param name="ignore_files_choice" type="select" label="Ignore files?" > 87 <param name="ignore_files_choice" type="select" label="Ignore files?" >
94 <option value="none" selected="true" >Include all files of selected classes in calculation</option> 89 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
95 </param> 90 </param>
96 <when value="none"> 91 <when value="none">
97 </when> 92 </when>
98 <when value="choose"> 93 <when value="choose">
99 <param name="ignore_files" type="text" label="ignore files" 94 <param argument="--ignore_files" type="text" label="ignore files"
100 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" /> 95 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
101 </when> 96 </when>
102 </conditional> 97 </conditional>
103 98
104 99
105 <conditional name="xgroups"> 100 <conditional name="xgroups">
106 <param name="xgroups" type="select" label="xgroups" > 101 <param name="xgroups" type="select" label="xgroups" >
107 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option> 102 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
108 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option> 103 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
109 </param> 104 </param>
110 <when value="all"> 105 <when value="choose">
106 <param name="xgroups_value" type="text" label="xgroup ids"
107 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
111 </when> 108 </when>
112 <when value="choose"> 109 <when value="all"/>
113 <param name="xgroups_value" type="text" label="xgroup ids"
114 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
115 </when>
116 </conditional> 110 </conditional>
117 111
118 112
119 <param name="purityType" type="select" label="Method of averaging purity" 113 <param argument="--purityType" type="select" label="Method of averaging purity"
120 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'"> 114 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
121 <option value="purityFWHMmedian" selected="true" >FWHM median</option> 115 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
122 <option value="purityFWHMmean" >FWHM mean</option> 116 <option value="purityFWHMmean" >FWHM mean</option>
123 <option value="purityFWmedian" >FW median</option> 117 <option value="purityFWmedian" >FW median</option>
124 <option value="purityFWmean" >FW mean</option> 118 <option value="purityFWmean" >FW mean</option>
125 </param> 119 </param>
126 120
127 <expand macro="camera_xcms" /> 121 <expand macro="camera_xcms" />
128 122
129 <param name="raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?" 123 <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
130 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used 124 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
131 the retention time correction tracking is slightly different to the other correction methods. To ensure 125 the retention time correction tracking is slightly different to the other correction methods. To ensure
132 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to 126 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
133 any retention time correction."/> 127 any retention time correction."/>
134 128